Probing the Structures of Viral RNA Regulatory Elements with SHAPE and Related Methodologies

Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA: a structural scaffold for nuclear, cytoplasmic and viral proteins

(2017) Joanna Sztuba-Solinska et al.   NUCLEIC ACIDS RESEARCH

A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8

(2016) Joanna Sztuba-Solinska et al.   NUCLEIC ACIDS RESEARCH

SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across theXistlncRNA in living cells

(2016) Matthew J. Smola et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA binding specificity of Ebola virus transcription factor VP30

(2016) Julia Schlereth et al.   RNA Biology

Design of a bioactive small molecule that targets r(AUUCU) repeats in spinocerebellar ataxia 10

(2016) Wang-Yong Yang et al.   Nature Communications

Small Molecule Targeting of a MicroRNA Associated with Hepatocellular Carcinoma

(2015) Jessica L. Childs-Disney et al.   ACS Chemical Biology

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

Selective small-molecule inhibition of an RNA structural element

(2015) John A. Howe et al.   NATURE

The HIV-1 Rev response element (RRE) adopts alternative conformations that promote different rates of virus replication

(2015) Chringma Sherpa et al.   NUCLEIC ACIDS RESEARCH

High-throughput, luciferase-based reverse genetics systems for identifying inhibitors of Marburg and Ebola viruses

(2014) Luke S. Uebelhoer et al.   ANTIVIRAL RESEARCH

Bottom-up Design of Small Molecules that Stimulate Exon 10 Skipping in MutantMAPTPre-mRNA

(2014) Yiling Luo et al.   CHEMBIOCHEM

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Functional long-range RNA–RNA interactions in positive-strand RNA viruses

(2014) Beth L. Nicholson et al.   NATURE REVIEWS MICROBIOLOGY

Gammaretrovirus mRNA expression is mediated by a novel, bipartite post-transcriptional regulatory element

(2014) Guy R. Pilkington et al.   NUCLEIC ACIDS RESEARCH

PAN’s Labyrinth: Molecular Biology of Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) PAN RNA, a Multifunctional Long Noncoding RNA

(2014) Cyprian Rossetto et al.   Viruses-Basel

The export receptor Crm1 forms a dimer to promote nuclear export of HIV RNA

(2014) David S Booth et al.   eLife

RNA-guided assembly of Rev-RRE nuclear export complexes

(2014) Yun Bai et al.   eLife

An Unusual Topological Structure of the HIV-1 Rev Response Element

(2013) Xianyang Fang et al.   CELL

A Lytic Viral Long Noncoding RNA Modulates the Function of a Latent Protein

(2013) M. Campbell et al.   JOURNAL OF VIROLOGY

Regulation of Viral and Cellular Gene Expression by Kaposi's Sarcoma-Associated Herpesvirus Polyadenylated Nuclear RNA

(2013) C. C. Rossetto et al.   JOURNAL OF VIROLOGY

The HIV-2 Rev-response element: determining secondary structure and defining folding intermediates

(2013) Sabrina Lusvarghi et al.   NUCLEIC ACIDS RESEARCH

Structural complexity of Dengue virus untranslated regions: cis -acting RNA motifs and pseudoknot interactions modulating functionality of the viral genome

(2013) Joanna Sztuba-Solinska et al.   NUCLEIC ACIDS RESEARCH

In-gel probing of individual RNA conformers within a mixed population reveals a dimerization structural switch in the HIV-1 leader

(2013) Julia C. Kenyon et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three-Dimensional RNA Structure of the Major HIV-1 Packaging Signal Region

(2013) James D. Stephenson et al.   STRUCTURE

Comparison of SIV and HIV-1 Genomic RNA Structures Reveals Impact of Sequence Evolution on Conserved and Non-Conserved Structural Motifs

(2013) Elizabeth Pollom et al.   PLoS Pathogens

RNA Secondary Structure Prediction Using High-throughput SHAPE

(2013) Sabrina Lusvarghi et al.   Jove-Journal of Visualized Experiments

Stability of a Long Noncoding Viral RNA Depends on a 9-Nt Core Element at the RNA 5' End to Interact with Viral ORF57 and Cellular PABPC1

(2012) Maria J. Massimelli et al.   International Journal of Biological Sciences

HIV-2 Genome Dimerization Is Required for the Correct Processing of Gag: a Second-Site Reversion in Matrix Can Restore Both Processes in Dimerization-Impaired Mutant Viruses

(2012) A. L'Hernault et al.   JOURNAL OF VIROLOGY

Exploring Ty1 retrotransposon RNA structure within virus-like particles

(2012) Katarzyna J. Purzycka et al.   NUCLEIC ACIDS RESEARCH

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

KSHV PAN RNA Associates with Demethylases UTX and JMJD3 to Activate Lytic Replication through a Physical Interaction with the Virus Genome

(2012) Cyprian C. Rossetto et al.   PLoS Pathogens

Identification ofCis-Acting Elements in the 3′-Untranslated Region of the Dengue Virus Type 2 RNA That Modulate Translation and Replication

(2011) Mark Manzano et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Kaposi's Sarcoma-Associated Herpesvirus Noncoding Polyadenylated Nuclear RNA Interacts with Virus- and Host Cell-Encoded Proteins and Suppresses Expression of Genes Involved in Immune Modulation

(2011) C. C. Rossetto et al.   JOURNAL OF VIROLOGY

Delineation of a core RNA element required for Kaposi's sarcoma-associated herpesvirus ORF57 binding and activity

(2011) Emi Sei et al.   VIROLOGY

A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression

(2011) Sumit Borah et al.   PLoS Pathogens

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

The RNA Transport Element of the MurinemusDRetrotransposon Requires Long-range Intramolecular Interactions for Function

(2010) Michal Legiewicz et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RNA Sequences and Structures Required for the Recruitment and Activity of the Dengue Virus Polymerase

(2010) Claudia V. Filomatori et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural basis for cooperative RNA binding and export complex assembly by HIV Rev

(2010) Matthew D Daugherty et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix

(2010) R. M. Mitton-Fry et al.   SCIENCE

Retroviral RNA Dimerization and Packaging: The What, How, When, Where, and Why

(2010) Silas F. Johnson et al.   PLoS Pathogens

Translational Regulation by the 3′ Untranslated Region of the Dengue Type 2 Virus Genome

(2009) Yan Wei et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Structure of the HIV-1 Rev response element alone and in complex with regulator of virion (Rev) studied by atomic force microscopy

(2009) Jesper Pallesen et al.   FEBS Journal

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE

HIV-1 Rev protein assembles on viral RNA one molecule at a time

(2009) S. J. K. Pond et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Highly Structured, Nuclease-Resistant, Noncoding RNA Produced by Flaviviruses Is Required for Pathogenicity

(2008) Gorben P. Pijlman et al.   Cell Host & Microbe

Structural and Functional Studies of the Promoter Element for Dengue Virus RNA Replication

(2008) M. F. Lodeiro et al.   JOURNAL OF VIROLOGY

Conformational Changes in the Solution Structure of the Dengue Virus 5' End in the Presence and Absence of the 3' Untranslated Region

(2008) C. Polacek et al.   JOURNAL OF VIROLOGY

A Solution to Limited Genomic Capacity: Using Adaptable Binding Surfaces to Assemble the Functional HIV Rev Oligomer on RNA

(2008) Matthew D. Daugherty et al.   MOLECULAR CELL

Resistance to RevM10 inhibition reflects a conformational switch in the HIV-1 Rev response element

(2008) M. Legiewicz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The capsid-coding region hairpin element (cHP) is a critical determinant of dengue virus and West Nile virus RNA synthesis

(2008) Karen Clyde et al.   VIROLOGY

Genome cyclization as strategy for flavivirus RNA replication

(2008) Sergio M. Villordo et al.   VIRUS RESEARCH